Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010996.1 Corchorus olitorius cultivar O-4 contig11028, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 894
Length: 1490
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 14--905 Score: 1228
Period size: 154 Copynumber: 5.8 Consensus size: 154
4 AGGCATAGAG
*
14 GGTTT-CCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGACACAAAATAACAAG
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAG
78 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGC-AAAATGATTATAGTTAGGCCA
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CTAAAATGATTATAGTTAGGCCA
* *
142 TAAACAATGGAAAGAAAGGCATCGA
130 TAAACAATGGAAAGAAAAGCATTGA
167 GGGTTT-CCAAATCGAAGACGATTCAAAACAGAACTAATGGGACCCCG-AAGGCACAAAATAACA
1 -GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGG-CCCCGAAAGGCACAAAATAACA
* * * *
230 AGTGTTCCAAATGAGCTAATACCTTCACAGTGGACTGATCTCACTAAAATGATTATACTTAGGCC
64 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCC
295 ATAAACAATGGAAAGAAAAGCATTGA
129 ATAAACAATGGAAAGAAAAGCATTGA
* ** * * * * *
321 GGTTTGCAAAATCGAAGACGATTCAAAA-ATTCACTAATGGGTCCTGATAGGCCCAAAATAACGA
1 GGTTTGCCAAATCGAAGACGATTCAAAACA-GAACTAATGGGCCCCGAAAGGCACAAAATAACAA
* * *
385 GTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCCA
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCA
450 TAAACAATGGAAA-AAAAGCATTGA
130 TAAACAATGGAAAGAAAAGCATTGA
* * * * *
474 GGTTTGTCAAATCGAACACGATTCAAAAC-GTCACTAATGGGCCCCGAAAGGCCCAAAATAATAA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGAAAGGCACAAAATAACAA
* ** ** *
538 GTGTTCCAAAGGAGCTAAAAACTTCACAAAGCCCTAATCTCAGC-AAAGTGATTATAGTTAGGCC
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CTAAAATGATTATAGTTAGGCC
**
602 ATAAACAATGGAAAGAAAAGCAACGA
129 ATAAACAATGGAAAGAAAAGCATTGA
* * **
628 GGATTGCCAAATCGAAGACGATTTAAAATGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAG
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAG
* *
693 TGTTCGAAATGAGGTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCAT
*
758 AAACAATGGAATGAAAAGCATTGA
131 AAACAATGGAAAGAAAAGCATTGA
* * * *
782 GGTTTGCCAAATCGAAGACGATTCAAAACA-AACTAAAGGGCCCTGATAGGTC-CAAAATTACAA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGG-CACAAAATAACAA
* * * * *
845 GTGTTCCAAATGAGCTTAAAACTTCACAATCGACTAATCTCACTAAAATTACTATAGTTAG
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
906 TGATGCGCCA
Statistics
Matches: 651, Mismatches: 75, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
153 224 0.34
154 421 0.65
155 6 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGA
Found at i:648 original size:307 final size:306
Alignment explanation
Indices: 19--893 Score: 1213
Period size: 307 Copynumber: 2.8 Consensus size: 306
9 TAGAGGGTTT
*
19 CCAAATCGAAGACGATTCAAAACA-GAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTC
1 CCAAATCGAAGACGATTCAAAA-ATGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTC
*
83 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACA
65 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
148 ATGGAAAGAAAGGCATCGAGGGTTT-CCAAATCGAAGACGATTCAAAACAGAACTAATGGGACCC
130 ATGGAAA-AAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGG-CCC
* * * ** * *
212 CG-AAGGCACAAAATAACAAGTGTTCCAAATGAGCTAATACCTTCACAGTGGACTGATCTCACTA
191 CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAGCACTAATCTCACTA
** *
276 AAATGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
256 AAATGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCAACGAGGATTG
* ** * * * * *
327 CAAAATCGAAGACGATTCAAAAATTCACTAATGGGTCCTGATAGGCCCAAAATAACGAGTGTTCC
1 CCAAATCGAAGACGATTCAAAAATGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCC
* *
392 AAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
457 TGGAAAAAAAGCATTGAGGTTTGTCAAATCGAACACGATTCAAAACGTCACTAATGGGCCCCGAA
131 TGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAA
* * * *
522 AGGCCCAAAATAATAAGTGTTCCAAAGGAGCTAAAAACTTCACAAAGCCCTAATCTCAGC-AAAG
195 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAGCACTAATCTCA-CTAAAA
*
586 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAACGAGGATTG
259 TGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCAACGAGGATTG
*
634 CCAAATCGAAGACGATT-TAAAATGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTC
1 CCAAATCGAAGACGATTCAAAAAT-GAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTC
* * *
698 GAAATGAGGTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACA
65 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * * *
763 ATGGAATGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAAACTAAAGGGCCCTGA
130 ATGGAA-AAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGA
* * * * *
828 TAGGTCCAAAATTACAAGTGTTCCAAATGAGCTTAAAACTTCAC-AATCGACTAATCTCACTAAA
194 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAGC-ACTAATCTCACTAAA
892 AT
258 AT
894 TACTATAGTT
Statistics
Matches: 496, Mismatches: 62, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
306 20 0.04
307 315 0.64
308 161 0.32
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (306 bp):
CCAAATCGAAGACGATTCAAAAATGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCC
AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
TGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAA
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAGCACTAATCTCACTAAAATG
ATTATACTTAGGCCATAAACAATGGAAAGAAAAGCAACGAGGATTG
Found at i:1038 original size:21 final size:21
Alignment explanation
Indices: 1012--1188 Score: 261
Period size: 21 Copynumber: 8.4 Consensus size: 21
1002 TGCTAGAAGT
1012 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
1033 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
1054 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
1075 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
1096 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
1117 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
1138 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
1159 TCATTGGAGAAGGTTTCCAAGC
1 TCATTGGAGAAGG-TTCCAAGC
1181 TCATTGGA
1 TCATTGGA
1189 AATGCCTAGA
Statistics
Matches: 147, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
20 4 0.03
21 126 0.86
22 17 0.12
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:1081 original size:63 final size:63
Alignment explanation
Indices: 1008--1188 Score: 303
Period size: 63 Copynumber: 2.9 Consensus size: 63
998 AAGATGCTAG
1008 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTCC
*
1071 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
*
1134 AAGTTCATTGGAG-AAGGTTCCAAGATCATTGGAGAAGGTTTCCAAGCTCATTGGA
1 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGG-TTCCAAGCTCATTGGA
1189 AATGCCTAGA
Statistics
Matches: 112, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
62 4 0.04
63 93 0.83
64 15 0.13
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (63 bp):
AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
Done.